tbuckley/cabot-search huggingface dataset:
Interleukin-33 Mediates Cardiomyopathy After Acute Kidney Injury by Signaling to Cardiomyocytes
Authors: Nans Florens, Rajesh K. Kasam, Valeria Rudman-Melnick, Suh-Chin Lin, Vikram Prasad, Jeffery D. Molkentin
Journal: Circulation (2023)

Acute kidney injury (AKI) is a short-term life-threatening condition that, if survived, can lead to renal insufficiency and development of chronic kidney disease. The pathogenesis of AKI and chronic kidney disease involves direct effects on the heart and the development of hypertrophy and cardiomyopathy.
CPSF6-mediated XBP1 3’UTR shortening attenuates cisplatin-induced ER stress and elevates chemo-resistance in lung adenocarcinoma
Authors: Chuandong Zhu, Yufeng Xie, Qiang Li, Zhiwei Zhang, Juan Chen, Kai Zhang, Xuefeng Xia, Danlei Yu, Dongqin Chen, Zhengyuan Yu, Jing Chen
Journal: Drug Resistance Updates (2023)
Continual learning strategies for cancer-independent detection of lymph node metastases
Authors: Péter Bándi, Maschenka Balkenhol, Marcory van Dijk, Michel Kok, Bram van Ginneken, Jeroen van der Laak, Geert Litjens
Journal: Medical Image Analysis (2023)

Recently, large, high-quality public datasets have led to the development of convolutional neural networks that can detect lymph node metastases of breast cancer at the level of expert pathologists. Many cancers, regardless of the site of origin, can metastasize to lymph nodes. However, collecting and annotating high-volume, high-quality datasets for every cancer type is challenging. In this paper we investigate how to leverage existing high-quality datasets most efficiently in multi-task settings for closely related tasks. Specifically, we will explore different training and domain adaptation strategies, including prevention of catastrophic forgetting, for breast, colon and head-and-neck cancer metastasis detection in lymph nodes. Our results show state-of-the-art performance on colon and head-and-neck cancer metastasis detection tasks. We show the effectiveness of adaptation of networks from one cancer type to another to obtain multi-task metastasis detection networks. Furthermore, we show that leveraging existing high-quality datasets can significantly boost performance on new target tasks and that catastrophic forgetting can be effectively mitigated.Last, we compare different mitigation strategies.
ClusterSeg: A crowd cluster pinpointed nucleus segmentation framework with cross-modality datasets
Authors: Jing Ke, Yizhou Lu, Yiqing Shen, Junchao Zhu, Yijin Zhou, Jinghan Huang, Jieteng Yao, Xiaoyao Liang, Yi Guo, Zhonghua Wei, Sheng Liu, Qin Huang, Fusong Jiang, Dinggang Shen
Journal: Medical Image Analysis (2023)
Agreement of respiratory viruses' detection between nasopharyngeal swab and bronchoalveolar lavage in adults admitted for pneumonia: a retrospective study
Authors: Donia Bouzid, Quentin Le Hingrat, Florian Salipante, Valentine Marie Ferré, Thierry Chevallier, Sarah Tubiana, Jean Christophe Lucet, Christophe Choquet, Yazdan Yazdanpanah, Jean François Timsit, Diane Descamps, Nadhira Houhou, Benoit Visseaux, Paul Loubet
Journal: Clinical Microbiology and Infection (2023)

The COVID-19 pandemic has highlighted the high diagnostic accuracy of the nasopharyngeal swab (including in intensive care unit (ICU) patients). This study aimed to compare nasopharyngeal swab and bronchoalveolar lavage (BAL) results for non-SARS-CoV-2 viruses in patients with suspected pneumonia.A retrospective analysis was performed in one French academic hospital on consecutive adults from 2012 to 2018 and tested nasopharyngeal swab and BAL within 24 hours by using multiplex PCR. The agreement in pathogen detection between nasopharyngeal swab and BAL was evaluated.Patients were primarily men (n = 178/276, 64.5%), with a median age of 60 years (IQR: 51-68 years). Of the 276 patients, 169 (61%) were admitted to the ICU for acute respiratory distress. We detected at least one respiratory virus in 34.4% of the nasopharyngeal swabs (n = 95/276) and 29.0% of BAL (n = 80/276). Two or more viruses were detected in 2.5% of the nasopharyngeal swabs (n = 7/276) and 2.2% of BAL (n = 6/276). Rhinovirus/enteroviruses were the most frequently detected viral group in 10.2% (n = 29/285) of the nasopharyngeal swabs and 9.5% (n = 27/285) of BAL, followed by influenza A, detected in 5.6% (n = 16/285) of the nasopharyngeal swabs and 4.9% (n = 14/285) of BAL. Overall agreement was 83.7% (n = 231/276 (95% CI [78.7%, 87.7%])) (i.e. same pathogen or pathogen combination was identified in the nasopharyngeal swab and BAL for 231 patients). Rhinovirus/enterovirus (n = 29/231) and respiratory syncytial virus (n = 13/231) had the lowest agreement of 62.1% (n = 18/29 (95% CI [42.4%-78.7%])) and 61.5% (n = 8/13 (95% CI [32.3%-84.9%])), respectively).There was a good agreement between nasopharyngeal swabs and BAL in detecting respiratory viruses among adult patients with suspected pneumonia. However, these data still encourage BAL in the case of a negative nasopharyngeal swab.
Corrigendum to “Sleep duration and metabolic syndrome: An updated systematic review and meta-analysis” [Sleep Med. Rev. 59 (2021) 101451]
Authors: Jing Xie, Yun Li, Yajun Zhang, Alexandros N. Vgontzas, Maria Basta, Baixin Chen, Chongtao Xu, Xiangdong Tang
Journal: Sleep Medicine Reviews (2023)
Driving pressure and adjunctive therapies in pulmonary sequelae of COVID-19 patients under invasive ventilation
Authors: Jessica González, Iván D. Benítez, Anna Motos, Antoni Torres, Ferran Barbé, Jordi de Batlle, Gerard Torres, David de Gonzalo-Calvo, Adrián Ceccato, Ricard Ferrer, Jordi Riera, Laia Fernández, Rosario Menéndez, José Ángel Lorente, Oscar Peñuelas, Dario García, Oriol Roca, Yhivian Peñasco, Pilar Ricart, Maria Cruz Martin Delgado, Luciano Aguilera, Alejandro Rodríguez, Maria Victoria Boado Varela, Felipe Pérez-García, Juan Carlos Pozo-Laderas, Jordi Solé-Violan, Ferran Roche-Campo, Mariana Andrea Novo, José Barberán, Rosario Amaya Villar, José Garnacho-Montero, Jose M. Gómez, Aaron Blandino Ortiz, Luis Tamayo Lomas, Alejandro Úbeda, Mercedes Catalán-González, Angel Sánchez-Miralles, Ignacio Martinez Varela, Ruth Noemí Jorge García, Nieves Franco, Victor D. Gumucio-Sanguino, Elena Bustamante-Munguira, Luis Jorge Valdivia, Jesús Caballero, Elena Gallego, Amalia Martínez de la Gándara, Alvaro Castellanos-Ortega, Josep Trenado, Judith Marin-Corral, Guillermo M. Albaiceta, Maria del Carmen de la Torre, Ana Loza-Vázquez, Pablo Vidal, Jose M. Añón, Cristina Carbajales Pérez, Victor Sagredo Nieves Carbonell, Lorenzo Socias, Carme Barberà, Angel Estella, Emili Diaz, Sally Santisteve, Adriano D. S. Targa, Clara Gort-Paniello, Anna Moncusí-Moix, Maria Aguilà, Fatty Seck
Journal: Intensive Care Medicine (2023)
Moral artificial intelligence and machine puritanism
Authors: Jean-François Bonnefon
Journal: Behavioral and Brain Sciences (2023)

Abstract Puritanism may evolve into a technological variant based on norms of delegation of actions and perceptions to artificial intelligence. Instead of training self-control, people may be expected to cede their agency to self-controlled machines. The cost–benefit balance of this machine puritanism may be less aversive to wealthy individualistic democracies than the old puritanism they have abandoned.
SARS-CoV-2 breakthrough infections in vaccinated individuals requiring ventilatory support for severe acute respiratory failure
Authors: Stefano Finazzi, Matilde Perego, Giovanni Tricella, Daniele Poole, V. Marco Ranieri, Caterina Rizzo, Roberto Fumagalli, Jorio Antonella, Petrucci Nicola, Della Selva Andrea, Tenio Rita, Cocciolo Francesco, Bonizzoli Manuela, Covani Frigieri Francesca, Giuntini Romano, Parrini Vieri, Bagalini Giampiero, Falini Stefano, Ciceri Rita, Giuntoli Monica, Alquati Omar, Faraldi Loredana, Giudici Riccardo, Parnigotto Alessandra, Di Pasquale Dino, Aurelio Cleto, Malacarne Paolo, Carli Manuela, Bottazzi Andrea, Babini Maria, Zani Gianluca, Zardin Michela, Mastroianni Alessandro, Peta Mario, Pero Alic.
Journal: Intensive Care Medicine (2023)
Spike Gene Target Amplification in a Diagnostic Assay as a Marker for Public Health Monitoring of Emerging SARS-CoV-2 Variants — United States, November 2021–January 2023
Authors: Heather M. Scobie, Akilah R. Ali, Philip Shirk, Zachary R. Smith, Prabasaj Paul, Clinton R. Paden, Norman Hassell, Xiao-yu Zheng, Anastasia S. Lambrou, Rebecca Kondor, Duncan MacCannell, Natalie J. Thornburg, Joseph Miller, Dave Wentworth, Benjamin J. Silk
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

Monitoring emerging SARS-CoV-2 lineages and their epidemiologic characteristics helps to inform public health decisions regarding vaccine policy, the use of therapeutics, and health care capacity. When the SARS-CoV-2 Alpha variant emerged in late 2020, a spike gene (S-gene) deletion (Δ69-70) in the N-terminal region, which might compensate for immune escape mutations that impair infectivity (1), resulted in reduced or failed S-gene target amplification in certain multitarget reverse transcription-polymerase chain reaction (RT-PCR) assays, a pattern referred to as S-gene target failure (SGTF) (2). The predominant U.S. SARS-CoV-2 lineages have generally alternated between SGTF and S-gene target presence (SGTP), which alongside genomic sequencing, has facilitated early monitoring of emerging variants. During a period when Omicron BA.5-related sublineages (which exhibit SGTF) predominated, an XBB.1.5 sublineage with SGTP has rapidly expanded in the northeastern United States and other regions.
Early Estimates of Bivalent mRNA Booster Dose Vaccine Effectiveness in Preventing Symptomatic SARS-CoV-2 Infection Attributable to Omicron BA.5– and XBB/XBB.1.5–Related Sublineages Among Immunocompetent Adults — Increasing Community Access to Testing Program, United States, December 2022–January 2023
Authors: Ruth Link-Gelles, Allison Avrich Ciesla, Lauren E. Roper, Heather M. Scobie, Akilah R. Ali, Joseph D. Miller, Ryan E. Wiegand, Emma K. Accorsi, Jennifer R. Verani, Nong Shang, Gordana Derado, Amadea Britton, Zachary R. Smith, Katherine E. Fleming-Dutra
Journal: MMWR Morbidity and Mortality Weekly Report (2023)

The SARS-CoV-2 Omicron sublineage XBB was first detected in the United States in August 2022.* XBB together with a sublineage, XBB.1.5, accounted for >50% of sequenced lineages in the Northeast by December 31, 2022, and 52% of sequenced lineages nationwide as of January 21, 2023. COVID-19 vaccine effectiveness (VE) can vary by SARS-CoV-2 variant; reduced VE has been observed against some variants, although this is dependent on the health outcome of interest. The goal of the U.S. COVID-19 vaccination program is to prevent severe disease, including hospitalization and death (1); however, VE against symptomatic infection can provide useful insight into vaccine protection against emerging variants in advance of VE estimates against more severe disease. Data from the Increasing Community Access to Testing (ICATT) national pharmacy program for SARS-CoV-2 testing were analyzed to estimate VE of updated (bivalent) mRNA COVID-19 vaccines against symptomatic infection caused by BA.5-related and XBB/XBB.1.5-related sublineages among immunocompetent adults during December 1, 2022–January 13, 2023. Reduction or failure of spike gene (S-gene) amplification (SGTF) in real-time reverse transcription–polymerase chain reaction (RT-PCR) was used as a proxy indicator of infection with likely BA.5-related sublineages and S-gene target presence (SGTP) of infection with likely XBB/XBB.1.5-related sublineages (2). Among 29,175 nucleic acid amplification tests (NAATs) with SGTF or SGTP results available from adults who had previously received 2–4 monovalent COVID-19 vaccine doses, the relative VE of a bivalent booster dose given 2–3 months earlier compared with no bivalent booster in persons aged 18–49 years was 52% against symptomatic BA.5 infection and 48% against symptomatic XBB/XBB.1.5 infection. As new SARS-CoV-2 variants emerge, continued vaccine effectiveness monitoring is important. Bivalent vaccines appear to provide additional protection against symptomatic BA.5-related sublineage and XBB/XBB.1.5-related sublineage infections in persons who had previously received 2, 3, or 4 monovalent vaccine doses. All persons should stay up to date with recommended COVID-19 vaccines, including receiving a bivalent booster dose when they are eligible.
Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients
Authors: Michael Tun Yin Lam, Sascha H. Duttke, Mazen F. Odish, Hiep D. Le, Emily A. Hansen, Celina T. Nguyen, Samantha Trescott, Roy Kim, Shaunak Deota, Max W. Chang, Arjun Patel, Mark Hepokoski, Mona Alotaibi, Mark Rolfsen, Katherine Perofsky, Anna S. Warden, Jennifer Foley, Sydney I. Ramirez, Jennifer M. Dan, Robert K. Abbott, Shane Crotty, Laura E. Crotty Alexander, Atul Malhotra, Satchidananda Panda, Christopher W. Benner, Nicole G. Coufal
Journal: Cell Reports Medicine (2023)

Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.
Zilucoplan in immune-mediated necrotising myopathy: a phase 2, randomised, double-blind, placebo-controlled, multicentre trial
Authors: Andrew L Mammen, Anthony A Amato, Mazen M Dimachkie, Hector Chinoy, Yessar Hussain, James B Lilleker, Iago Pinal-Fernandez, Yves Allenbach, Babak Boroojerdi, Mark Vanderkelen, Eumorphia Maria Delicha, Harold Koendgen, Ramin Farzaneh-Far, Petra W Duda, Camil Sayegh, Olivier Benveniste
Journal: The Lancet Rheumatology (2023)
Autoantibodies against citrullinated and native proteins and prediction of rheumatoid arthritis-associated interstitial lung disease: a nested case–control study
Authors: Vanessa L Kronzer, Keigo Hayashi, Kazuki Yoshida, John M Davis, Gregory C McDermott, Weixing Huang, Paul F Dellaripa, Jing Cui, Vivi Feathers, Ritu R Gill, Hiroto Hatabu, Mizuki Nishino, Rachel Blaustein, Cynthia S Crowson, William H Robinson, Jeremy Sokolove, Katherine P Liao, Michael E Weinblatt, Nancy A Shadick, Tracy J Doyle, Jeffrey A Sparks
Journal: The Lancet Rheumatology (2023)
Prone position for acute respiratory distress syndrome and the hazards of meta-analysis
Authors: D. Poole, A. Pisa, R. Fumagalli
Journal: Pulmonology (2023)

Researchers have tried unsuccessfully for many years using randomized controlled trials to show the efficacy of prone ventilation in treating ARDS. These failed attempts were of use in designing the successful PROSEVA trial, published in 2013. However, the evidence provided by meta-analyses in support of prone ventilation for ARDS was too low to be conclusive. The present study shows that meta-analysis is indeed not the best approach for the assessment of evidence as to the efficacy of prone ventilation. We performed a cumulative meta-analysis to prove that only the PROSEVA trial, due to its strong protective effect, has substantially impacted on the outcome. We also replicated nine published meta-analyses including the PROSEVA trial. We performed leave-one-out analyses, removing one trial at a time from each meta-analysis, measuring p values for effect size, and also the Cochran's Q test for heterogeneity assessment. We represented these analyses in a scatter plot to identify outlier studies influencing heterogeneity or overall effect size. We used interaction tests to formally identify and evaluate differences with the PROSEVA trial. The positive effect of the PROSEVA trial accounted for most of the heterogeneity and for the reduction of overall effect size in the meta-analyses. The interaction tests we conducted on the nine meta-analyses formally confirmed the difference in the effectiveness of prone ventilation between the PROSEVA trial the other studies. The clinical lack of homogeneity between the PROSEVA trial design and the other studies should have discouraged the use of meta-analysis. Statistical considerations support this hypothesis, suggesting that the PROSEVA trial is an independent source of evidence.
Prenatal Exposure to PM2.5 Oxidative Potential and Lung Function in Infants and Preschool- Age Children: A Prospective Study
Authors: Anouk Marsal, Rémy Slama, Sarah Lyon-Caen, Lucille Joanna S. Borlaza, Jean-Luc Jaffrezo, Anne Boudier, Sophie Darfeuil, Rhabira Elazzouzi, Yoann Gioria, Johanna Lepeule, Ryan Chartier, Isabelle Pin, Joane Quentin, Sam Bayat, Gaëlle Uzu, Valérie Siroux
Journal: Environmental Health Perspectives (2023)

Background: Fine particulate matter (PM2.5) has been found to be detrimental to respiratory health of children, but few studies have examined the effects of prenatal PM2.5 oxidative potential (OP) on lung function in infants and preschool children. Objectives: We estimated the associations of personal exposure to PM2.5 and OP during pregnancy on offspring objective lung function parameters and compared the strengths of associations between both exposure metrics. Methods: We used data from 356 mother–child pairs from the SEPAGES cohort. PM filters collected twice during a week were analyzed for OP, using the dithiothreitol (DTT) and the ascorbic acid (AA) assays, quantifying the exposure of each pregnant woman. Lung function was assessed with tidal breathing analysis (TBFVL) and nitrogen multiple-breath washout (N2MBW) test, performed at 6 wk, and airwave oscillometry (AOS) performed at 3 y. Associations of prenatal PM2.5 mass and OP with lung function parameters were estimated using multiple linear regressions. Results: In neonates, an interquartile (IQR) increase in OPvDTT (0.89 nmol/min/m3) was associated with a decrease in functional residual capacity (FRC) measured by N2MBW [β=−2.26mL; 95% confidence interval (CI): −4.68, 0.15]. Associations with PM2.5 showed similar patterns in comparison with OPvDTT but of smaller magnitude. Lung clearance index (LCI) and TBFVL parameters did not show any clear association with the exposures considered. At 3 y, increased frequency-dependent resistance of the lungs (Rrs7–19) from AOS tended to be associated with higher OPvDTT (β=0.09 hPa×s/L; 95% CI: −0.06, 0.24) and OPvAA (IQR=1.14 nmol/min/m3; β=0.12 hPa×s/L; 95% CI: −0.04, 0.27) but not with PM2.5 (IQR=6.9 μg/m3; β=0.02 hPa×s/L; 95% CI: −0.13, 0.16). Results for FRC and Rrs7–19 remained similar in OP models adjusted on PM2.5. Discussion: Prenatal exposure to OPvDTT was associated with several offspring lung function parameters over time, all related to lung volumes. https://doi.org/10.1289/EHP11155
The vicious cycle of biophobia
Authors: Masashi Soga, Kevin J. Gaston, Yuya Fukano, Maldwyn J. Evans
Journal: Trends in Ecology & Evolution (2023)

People can express irrational fears and disgust responses towards certain wild organisms. This so-called 'biophobia' can be useful and indeed necessary in some circumstances. Biophobia can, however, also lead to excessive distress and anxiety which, in turn, can result in people avoiding interactions with nature. Here, we highlight concern that this reduction in interactions with nature might lead to progressive increases in biophobia, entrenching it more in individuals and across society. We propose the 'vicious cycle of biophobia', a concept that encapsulates how excessive aversion towards nature might emerge and grow in society. The vicious cycle of biophobia risks accelerating the extinction of experience, leading to long-term adverse consequences for the conservation of biodiversity.
Soy-Based Infant Formula Feeding and Uterine Fibroid Development in a Prospective Ultrasound Study of Black/African-American Women
Authors: Christine R. Langton, Quaker E. Harmon, Kristen Upson, Donna D. Baird
Journal: Environmental Health Perspectives (2023)

Background: Uterine fibroids are highly prevalent, benign tumors. They are the leading indication for hysterectomy, and Black women are disproportionally burdened. Soy-based infant formula contains phytoestrogens, and exposure during sensitive developmental windows may adversely affect the developing uterus; early phytoestrogen treatment in rodent studies led to detrimental uterine effects, including increased fibroid risk in Eker rats. Limited epidemiological studies also have suggested increased fibroid development with soy formula infant feeding. Objective: The goal of this study was to examine the association between soy formula feeding in infancy and fibroid development in adulthood. Methods: We evaluated this association among 1,610 Black/African-American women age 23–35 y in the Study of Environment, Lifestyle & Fibroids (SELF). Soy formula feeding data was gathered directly from the participants' mothers (89%). A standardized ultrasound examination was conducted during 4 clinic visits over 5 y to detect fibroids ≥0.5cm in diameter. We used Cox proportional hazards regression to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between soy formula feeding and incident fibroids adjusted for early-life and adult factors. Fibroid growth was calculated as change in log-volume for fibroids matched at successive visits. Results: Of 1,121 fibroid-free participants at baseline, 150 (13%) were ever fed soy formula as infants, and 269 (24%) developed incident fibroids. We did not observe an association between ever being fed soy formula and incident fibroid risk (HR=1.08; 95% CI: 0.75, 1.54). However, participants fed soy formula within 2 months of birth and for >6 months (n=53) had an elevated risk of fibroid incidence in comparison with those never fed soy formula (HR=1.56; 95% CI: 0.92, 2.65). Fibroid growth rates did not differ. Discussion: Adding support to limited human data, this prospective fibroid study found that soy-based formula feeding during infancy was associated with a suggestive increase in risk of ultrasound-identified incident fibroids in adulthood. https://doi.org/10.1289/EHP11089
Exposure to Air Pollution during Pre-Hypertension and Subsequent Hypertension, Cardiovascular Disease, and Death: A Trajectory Analysis of the UK Biobank Cohort
Authors: Shiyu Zhang, Zhengmin Min Qian, Lan Chen, Xing Zhao, Miao Cai, Chongjian Wang, Hongtao Zou, Yinglin Wu, Zilong Zhang, Haitao Li, Hualiang Lin
Journal: Environmental Health Perspectives (2023)

The associations between air pollution exposure and morbidity and mortality of cardiovascular diseases (CVDs) have been widely reported; however, evidence on such associations across different dynamic disease trajectories remain unknown.